I don't have a solution for you, but I just wanted to bump this as I've also experienced the problem. However, its not just zip files that were affected for me, the entire webmail became unusable and all the pages came down as weird glyphs. This was using sm4 on IIS5
I assume from this that smartermail is using its own gzipping and that the two combined meant that the browser was deflating one layer of compression but not the other? Actually, I notice using YSlow with Firebug that login.aspx is gzipped.
This may become a problem for us when our clients want gzip compression on their aspx pages as we can't set it on a per site basis.
Any way to turn off the built-in compression in SM4?